Contacts of the helix formed by residues 1434 - 1440 (chain G) in PDB entry 6C3P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR1434 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1433G GLY* 1.3 73.0 - - - -
1435G ILE* 1.3 60.0 + - - +
1436G ARG* 3.8 13.7 - - + -
1437G PHE* 2.8 24.0 + - + +
1438G ASN* 2.4 43.6 + - - +
1470G LEU 3.2 1.7 + - - -
1471G ASP* 3.0 26.1 + - - +
1472G ALA 3.0 20.5 + - - -
1473G ILE* 5.7 1.3 - - - -
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Residues in contact with ILE1435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434G THR* 1.3 77.8 + - - +
1436G ARG* 1.3 60.1 + - - +
1438G ASN* 3.8 6.1 - - + +
1439G LEU* 2.9 47.7 + - + +
1450G LEU* 5.8 0.4 - - + -
1454G LEU* 4.7 11.4 - - + -
1463G VAL* 5.8 4.3 - - + -
1466G LEU* 6.5 2.2 - - + -
1470G LEU* 3.2 49.1 - - + +
1471G ASP 4.6 0.2 - - - +
1472G ALA* 5.1 7.4 - - + +
1474G ILE* 4.0 27.8 - - + -
1481G PHE* 6.0 1.8 - - + -
1489G PHE* 4.1 23.1 - - + -
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Residues in contact with ARG1436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434G THR* 3.2 11.9 - - + -
1435G ILE* 1.3 77.4 - - - +
1437G PHE* 1.3 57.1 + - - +
1440G ASP* 2.7 39.4 + - + +
1447G ASP* 2.7 43.9 + - - -
1450G LEU* 3.8 13.7 - - - -
1469G GLY 5.3 0.6 + - - -
1470G LEU* 3.2 22.4 + - + +
1471G ASP* 3.9 24.7 + - - +
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Residues in contact with PHE1437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501G GLU* 5.9 0.9 - - - -
517G ILE* 5.8 0.9 - - + -
518G PHE* 3.5 33.0 - + - -
521G ARG* 3.3 54.3 - - - -
1431G PHE* 4.3 20.5 - + + +
1432G SER 4.1 17.7 - - - -
1433G GLY* 4.4 6.5 - - - -
1434G THR* 2.8 24.9 + - + +
1436G ARG* 1.3 75.8 - - - +
1438G ASN* 1.3 65.3 + - - +
1439G LEU 3.5 0.2 + - - -
1440G ASP 3.5 19.8 - - - +
1441G PRO* 3.9 14.4 - - + +
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Residues in contact with ASN1438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514G TRP* 4.6 2.9 - - - -
1430G LEU* 5.1 1.3 - - + +
1431G PHE* 2.3 59.2 + - + +
1433G GLY* 3.6 4.2 - - - +
1434G THR* 2.4 49.8 + - - +
1435G ILE* 3.5 8.6 + - + +
1437G PHE* 1.3 70.9 - - - +
1439G LEU* 1.3 63.7 + - + +
1474G ILE* 3.1 28.8 - - + +
1489G PHE* 6.5 0.4 - - + -
1493G ARG* 3.4 23.4 + - - +
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Residues in contact with LEU1439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514G TRP* 3.9 11.1 - - - -
1435G ILE* 2.9 38.0 + - + +
1436G ARG 4.4 0.2 - - - +
1438G ASN* 1.3 81.2 - - + +
1440G ASP* 1.3 66.9 + - - +
1441G PRO* 3.1 12.4 - - - +
1450G LEU* 3.9 32.1 - - + +
1453G ALA* 5.5 2.0 - - + -
1454G LEU* 4.7 12.8 - - + -
1489G PHE* 4.3 10.3 - - + +
1492G ALA* 4.2 7.0 - - + -
1493G ARG* 3.5 40.7 - - + +
1496G VAL* 4.0 19.7 - - + +
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Residues in contact with ASP1440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1436G ARG* 2.7 27.8 + - - +
1437G PHE* 3.5 12.0 - - - -
1439G LEU* 1.3 76.6 - - - +
1441G PRO* 1.3 64.9 - - - +
1442G GLU 2.9 21.9 - - - +
1443G ARG* 4.8 3.3 - - - -
1445G CYS* 3.2 38.4 + - - +
1450G LEU* 3.2 31.1 - - - +
1496G VAL* 3.8 11.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il